Problem: Engine noise through tower speakers

I recently hooked up my tower speaker and sub but when i put it in the water the other day i have the whining engine noise through the tower speakers. I know what it is but i need to know how to fix it. I have tried the RCA filter and it works......but....when the filter is on my sub barley moves and you cannot tell its working. Anyone had this happen or know how to fix it??? Thanks in advance.